agustaboy, depending on how much interference you are expecting to the inner fender housing there are a couple simple tricks to move the engine and transaxle forward to consider that may be preferable to cutting into the chassis structure.
If you only need approximately 3/4" you can bend the tranny mounts into an "S" shape. This is typically done to move the transaxle aft, but I don't see why it couldn't be used to move it forward. If you need more than that you may need to fab new trans mounts. Ford Big Block swaps typically move the transaxle ~3" from neutral; I have not heard of problems with this amount of misalignment, but I would expect increased U-joint friction and stress with increasing misalignment.
You may also be able to move just the engine forward by putting a spacer between the bellhousing and engine. I have seen approximately 1" (?) thick adapters used with engine swaps. I am also using a QuickTime bellhousing and found it preferable to use a hydraulic throwout bearing rather than fabricating the clutch actuator slave mount.
For clearance up front I fabricated an alternator/AC mount and used an aftermarket pulley to suck these accessories as close as possible to the engine. I also used an electric water pump, mounted behind the radiator. I added 1/4" thick wooden strips (and longer bolts) to space-out the firewall access door.
Every Ford Big Block conversion that I have seen cuts into the wheel house structure, like you are planning. By using a few tricks I was able to keep the structure unmodified and fit the much longer/larger Big Block with the transaxle in the "stock" location.
Thank you for posting your project. It is fun to see your work and problem-solving.